I had 6 minutes left to travel, after checking an message then re-entering the cockpit it said 11 minutes, this kind of thing happens a lot to me, sometimes have hours added to hyper travel. it doesn't seem to matter the length of my journey, as long as it's over 1 hour long the ETA does it's own thing. Is this normal? Or is it because my ship piloting is only 2?

I thought your travel was calculated when you set the course, not recalculated as you go along.

A few minutes difference is because of the way time is calculated in SWC - its done every 3 minutes, and the ETA on the side bar takes this number from the server when you load the page then counts itself down. When you load a new page, it looks again and resets itself.

As for adding hours on, that sounds like a bug. There have been issues before with travel getting frozen for a bit, so ti maybe that you've hit those every so often.